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    <title>Mapping-QC</title>
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    <h1>
      <strong>Mapping-QC : pSEVA uses SAMStat for Mapping-QC. </strong>
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      <strong>SAMStat</strong>
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    <p>
    	SAMStat reports nucleotide composition, length distribution, base quality distribution, mapping statistics, mismatch, insertion and deletion error profiles, di-nucleotide and 10-mer over-representation.
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    	Lassmann et al. (2010) "SAMStat: monitoring biases in next generation sequencing data." Bioinformatics doi:10.1093/bioinformatics/btq614 [PMID: 21088025]
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        <strong>SAMStat Options</strong>
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Input File Name &nbsp;&nbsp;&nbsp;<input type="file" size="80" name="InputFile"/>      
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;prints summary statistics of multiple libraries into one file(s) &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="samstat_s" />
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;treat all reads mapping more than k errors as unmapped(k) &nbsp;&nbsp;<input type="text" size="10" name="samstat_k" />
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;name of library and output file when reading from stdin(n) &nbsp;&nbsp; <input type="text" size="10" name="samstat_n" />
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;specifies the format when reading from stdin(f) &nbsp;&nbsp; <input type="text" size="10" name="samstat_f" />
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;filter used in samtools(F) &nbsp;&nbsp; <input type="text" size="10" name="samstat_F" value="768"/>
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